BabcockHall

I decided to try a test run today. The stacking gel is only a few millimeters in length. I started at 150 volts and about 60 milliamps, and it seemed as if the current decreased over time. The gel ran more quickly than what I was used to. I am destaining the gel now, and the bands look good.

I am trying precast gels for the first time, and it is for a laboratory class. I talked to someone in technical services, and he sent a pdf with some instructions. As I read them, I did not see anything about changing the voltage between the stacking gel and the resolving gel. I will try something similar to what you suggest.

I have cast and used SDS PAGE with Tris/glycine/SDS electrode buffer. However, I was planning to use some precast, gradient gels for the first time. I am trying to contact the manufacturer, but I have not yet heard back. "BisTris" is in the product description, and the catalog page mentions the possibility of ordering MES or MOPS buffer. My first question is whether I should change my recipe for the sample loading buffer. My old recipe includes Tris (pH 6.8, same as stacking gel), SDS, 2-mercaptoethanol, glycerol, and bromphenol blue. My second question is what sort of power settings should I use? In the past I have typically used about 100 volts during the stacking portion of the run, which changes to 150 volts or more volts once the samples enter the resolving gel.

I tried the option of print to pdf today. I chose the landscape option. I still cannot fill more than about half the page with the spectrum. On the other hand, I was able to get better results with Microsoft's Snip tool than I had previously: I resized the scan within the Cary software. I will keep working on this.Fraction_17_gelfiltration_landscape.pdfFraction_17_gelfiltration_landscape.pdf

Thank you; this is helpful in a couple of ways. One, it notes that one cannot directly export the spectrum as a jpg or png, which is what I thought. Two, it confirms that the spectrum can be exported as a csv file. The problem with csv files is that they take a bit of editing before one gets a usable spectrum (this is not ideal in a classroom application).

After a long hiatus, I am using Cary spectrophotometers again. I am struggling to find the best way to export just a spectrum electronically, especially an electronic format that could be imported into a Word document. As a work-around, I used Microsoft's Snip and Sketch tool (not sure that this is the correct name) to make .jpg or .png files, but this is an imperfect solution. When I tried to export the Report as a .pdf file, I obtained the spectrum plus parameters, and for right now, it is just the spectrum that I want. I tried two other formats, .DSW and .RTF, but I was not successful. The details escape me at the moment, but I will try to return to this question later. For a very different program I used .wmf format (Windows Meta File), but that is not available in this instance. Any thoughts? Thank you in advance.

The assays that I have in mind are disk diffusion assays and assays to determine minimum inhibitory concentration or related. Sometimes these assays are conducted in rich medium (Luria broth, Terrific Broth, or similar). It seems to me that this choice biases against finding inhibitors that target enzymes whose absence is conditionally lethal. If one inhibits an enzyme that produces a metabolite that can be obtained from the medium, then growth of the cells might be impaired little or not at all. If one is interested in developing an antimicrobial compound, perhaps using a medium that mimics human serum is a better choice, but I imagine that there are complications I doubt very much that I am the only person who has wondered about this possible problem. Are there any papers that touch upon this subject or address it in a systematic manner.

Faucher and Maitre Synthetic Communications 2003 33(20):3503-3511. DOI:10.1081/SCC-120024730 I would consider the possibility that TCEP is reducing DMSO, although the presence of iodine may be necessary for a rapid reaction (see Faucher and Maitre). If I could find no more information on this topic, I would consider switching my solvent to DMF. Is there any reason that you are using TCEP and not 2-ME or DTT as your reducing agent?

Tutoring is not a replacement for studying on your own, IMO. It can fill in the gaps when you get stuck. My advice is to turn off all electronic distractions; short, intense studying is more effective than long periods of diffuse studying.

If I recall correctly I once used bromocresol green to detect compounds containing a carboxylic acid group on a TLC plate. That is probably different from the sort of reaction that you were thinking about.

A catalyst such as thiamine pyrophosphate can decarboxylate alpha-keto acids.

Hi CharonY, Thank you for a very helpful answer. We used established antimicrobial substances as positive controls; we were not comparing our compounds to them in any other sense.

Many covalent inhibitors are irreversible, but not all of them are. If each step to form a covalent bond is reversible, then the whole process is reversible. A good example is peptide aldehyde or trifluromethylketone binding to the nucleophile in a cysteine or serine proteases. Reversible, covalent inhibitors seem to be catching on, so it's a good topic.

My suggestion is to rewrite the standard Michaelis-Menten equation in the form (velocity)/Vmax = and so forth. To do so is trivial from the point of view of the algebra involved.

Good Morning, We are collaborating with a group that performs disk diffusion assays on compounds that we make. We would like to publish some disk diffusion data in addition to reporting on the syntheses and perhaps the in vitro behavior of a set of compounds. However, the area of whole-cell biological testing is generally unfamiliar to me, and I don't know how to present data in a manuscript. I also don't have a good feel for what information should or should not be included in reporting these data. Perhaps someone could suggest a model publication, for example. Thank you.

In carbohydrate chemistry, my suggestion is generally to start with the HC-1 signal, because it verifies the configuration of this carbon. It is also simpler in appearance.

We have tried both diethyl amine and 4-methylpiperidine in the deprotection. Most recently we removed the white precipitate with centrifugation in Corex centrifuge tubes. This was an improvement over having a bunch of precipitate sit on the top of the silica column.

The carbon and oxygen are still present. What do you think happens to the hydrogen on the oxygen?

Is there any point in repeating a successful disk diffusion assay at lower starting concentration of substance? Or would it make more sense to move to some form of minimum inhibitory concentration assays?

We tried a silica column after using diethyl amine to deprotect. We obtained two pools, but we did not obtain our product. We are short on mass. It seems like time for a rethink regarding the best purification method.

We have a tertiary-butyl protected amino acid in which nitrogen is protected with FMOC. We removed the FMOC group with diethyl amine, and we used rotary evaporation plus a toluene strip to remove the volatiles. We attempted to purify over a short column of silica. We were able to remove a fast-moving impurity (presumably dibenzofulvene or a derivative) using 40:60 EtOAc/hexanes, then switched to 99:1 hexanes/TEA in the hope of eluting the N-deprotected product, still bearing the carboxylate protecting group, but the product was not soluble in EtOAc or in DCM (it might have been a suspension). We eluted with 90:10 DCM/methanol and saw two products by TLC. They were not completely separated. I am interested in soliciting ideas for what we should do differently next time. In retrospect a lower percentage of methanol would have been an improvement. I wonder whether or not the solubility of the amine would have been better in chloroform than it was in DCM. I realize that some people do not purify at all at this stage, but instead couple the crude product with another amino acid. We also want to couple to another amino acid.

https://doi.org/10.1002/chem.201101163 I am working on synthetic routes to a glucoside. The beta-trimethylsilylethoxymethyl (SEM) group has some attractive features (particularly in regards to deprotection), but I have only found one paper in which four SEM groups were used to protect the oxygen atoms at carbons 2-4 and 6 of a glycoside conjugated with a steroid. They did not deprotect to the best of my knowledge, but I assume that one would use a standard recipe. I did find a paper in which a glycoside was protected with several different groups, including one SEM. Are there disadvantages to using the SEM group as the protecting group? Are there reasons why it has been used more in carbohydrate chemistry? Should I be favoring other protecting groups instead?

You might be able to do it using what is called the specific activity of the enzyme. Specific activity is given as units per milligram of protein. The denominator is a mass, not a concentration.

Does anyone know of a web-based program for estimating retention times that is simple to use? I found one, but I struggled a bit with the output.

Our interest is in LC/MS of the peptides, and we plan to work in water/acetonitrile/formic acid. We found a number of protocols for C-18 on line (I can provide links to these), and we are focusing on those protocols that specify formic acid (not TFA). Our Zip Tips use C-18. (1) Are Zip Tips necessary? (2) Given their capacity, does one obtain enough for material for one or for several LC/MS runs? (3) Are Zip Tips reusable? (4) Does anyone have a paper or protocol that is especially informative? Thank you very much.